There are some very interesting properties of a Bose-Einstein Condensate (BEC)...

When the JILA team raised the magnetic field strength still further, the condensate suddenly reverted to attraction, imploded and shrank beyond detection, and then exploded, expelling off about two-thirds of its 10,000 or so atoms. About half of the atoms in the condensate seemed to have disappeared from the experiment altogether, not being seen either in the cold remnant or the expanding gas cloud.

Carl Wieman explained that under current atomic theory this characteristic of Bose–Einstein condensate could not be explained because the energy state of an atom near absolute zero should not be enough to cause an implosion...

Staff: Mentor

That's what I asked. What happened to those protons and electorns of the disappeared atoms.

Were they conserved?

Yes, they were just not detected. If you had read the Wikipedia entry, you would have seen after twhat OCR quoted:

Most likely they formed molecules consisting of two bonded rubidium atoms.

Also, the statement

When a substance is cooled closer to 0K, it will for Bose-Einstein Condensate

is mostly false. When a substance is cooled [Edit: to a low enough temperature], it forms a solid [Edit: with the exception of helium, which becomes superfluid]. Only in very special cases, such as for dilute gases, does a bunch of bosons can be coerced to form a BEC. It is not trivial to do!